Compositions and methods for glioblastoma treatment

ABSTRACT

The present disclosure concerns an oncolytic virus for the treatment of cancer, such as in brain cancer, for example glioblastoma. The oncolytic virus may exhibit reduced levels of neurotoxicity. The oncolytic virus may be an isolated viral particle capable of producing a cDNA polynucleotide that includes a sequence according to SEQ ID NO: 1 when the virus is in a host cell. The oncolytic virus may be an isolated viral particle that includes an RNA polynuclotide that includes a sequence according to SEQ ID NO: 2. The oncolytic virus may be an isolated viral particle having a genome that includes open reading frames that encode: proteins having sequences comprising SEQ ID NOs: 3, 4, 5, 6 and 7; or variants thereof.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 14/123,057 filed Nov. 27, 2013, which is a national phase entry of PCT/CA2012/050385 filed on Jun. 7, 2012, which claims priority to U.S. Provisional Patent Application No. 61/494,628 filed Jun. 8, 2011, which are all incorporated herein by reference.

FIELD

The present disclosure relates to rhabdoviruses and their use as an oncolytic treatment. More specifically, the present disclosure relates to Farmington rhabdovirus and its use in the treatment of glioblastoma.

BACKGROUND

This section provides background information related to the present disclosure which is not necessarily prior art.

Brain cancer is the leading cause of cancer-related death in patients younger than age 35 and accounts for roughly 10% of all cancers diagnosed in North America. Treatment of brain tumours is complicated by the fact that there are more than 120 different types, which range from low grade astrocytomas to high grade glioblastomas (GBM). Malignant gliomas, such as GBM, are by far the most common brain cancer found in adults and one of the most difficult to treat. Even with aggressive single and multimodal treatment options such as surgery, chemotherapy, radiation and small molecule inhibitors, the survival has remained unchanged over the past three decades with a median survival of less than one year after diagnosis. Reasons for the failure of conventional treatments is multifactorial including the highly infiltrative/invasive nature of GBM, limitation of drug delivery through the blood brain barrier and neural parenchyma, and genetic heterogeneity resulting in intrinsic resistance to available treatments and the rise of aggressive resistant clones. Therefore, there is a dire requirement for new treatment options, which has led to the renaissance of oncolytic viral therapy for GBM.

Currently, the efficacy and safety of several oncolytic viruses with various tumour targeting strategies are being evaluated in the lab and clinic against GBM. The rhabdovirus vesicular stomatitis virus (VSV) constitutes one of these efficacious viruses being tested preclinically. However, a desired route of viral administration for GBM is intracerebral delivery, which is not currently possible with VSV due to its neurotoxicity.

SUMMARY

It is an object of the present disclosure to obviate or mitigate at least one disadvantage of previous oncolytic viruses. For example, the oncolytic virus of the present disclosure may exhibit reduced levels of neurotoxicity.

The present technology includes systems, methods, processes, articles, and compositions that relate to rhabdoviruses, such as Farmington rhabdovirus, and related nucleotide and protein sequences thereof, and the use of such in oncolytic treatments, for example treatments for glioblastoma.

According to one aspect of the present disclosure, there is provided an isolated viral particle capable of producing a cDNA polynucleotide that includes a sequence according to SEQ ID NO: 1 when the virus is in a host cell.

According to another aspect of the present disclosure, there is provided an isolated viral particle that includes an RNA polynuclotide that includes a sequence according to SEQ ID NO: 2.

According to still another aspect of the present disclosure, there is provided an isolated viral particle having a genome that includes open reading frames that encode: a protein having a sequence comprising SEQ ID NO: 3, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 4, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 5, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 6, or a variant thereof; and a protein having a sequence comprising SEQ ID NO: 7, or a variant thereof.

The variant of a reference protein may be a protein that has a sequence which is at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the sequence of the reference protein, and where the variant protein maintains the same biological function as the reference protein.

In some examples, at least one of the open reading frames encodes a protein having a sequence which is a sequence selected from the group consisting of SEQ ID NOs: 3, 4, 5, 6, and 7. In such examples, the variant of a reference protein may be a protein having a sequence which is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the sequence of the reference protein, and where the variant protein maintains the same biological function as the reference protein.

The viral genome may include open reading frames that encode: a protein having a sequence comprising SEQ ID NO: 3; a protein having a sequence comprising SEQ ID NO: 4; a protein having a sequence comprising SEQ ID NO: 5; a protein having a sequence comprising SEQ ID NO: 6; and a protein having a sequence comprising SEQ ID NO: 7.

The isolated viral particle may further include at least one additional open reading frame for encoding at least one additional protein. The additional protein may be an immunogenic protein.

According to another aspect of the present disclosure, there is provided an isolated viral particle capable of producing a cDNA polynucleotide when the virus is in a host cell, the cDNA polynucleotide having a sequence that includes: SEQ ID NO: 8, or a conservative variant thereof; SEQ ID NO: 9, or a conservative variant thereof; SEQ ID NO: 10, or a conservative variant thereof; SEQ ID NO: 11, or a conservative variant thereof; SEQ ID NO: 12, or a conservative variant thereof; and promoters thereof.

The conservative variant of a sequence of nucleotides may be a sequence that is at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the reference sequence of nucleotides. The conservative variant may be a sequence comprising one or more silent substitutions.

According to still another aspect of the present disclosure, an isolated viral particle according to the present disclosure may be used for the treatment of cancer. The cancer may be a brain cancer. The brain cancer may be a glioblastoma. The isolated viral particle may be used to infect a cell where the infected cell is for the treatment of cancer.

According to still another aspect of the present disclosure, an isolated viral particle according to the present disclosure may be used for inducing an immunogenic response in a person administered the virus. The immunogenic response may be an anti-cancer response. The isolated viral particle may be used to infect a cell where the infected cell is use to generate the immunogenic response.

The isolated viral particle may be formulated for direct delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The isolated viral particle may be formulated for administration via intrathecal, intravenous or intracranial injection.

The infected cell may be formulated for direct delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The infected cell may be formulated for administration via intrathecal, intravenous or intracranial injection.

According to still another aspect of the present disclosure, there is provided a method for treating cancer comprising administering an isolated viral particle according to the presente disclosure to a patient having cancer. The cancer may be a brain cancer. The brain cancer may be a glioblastoma.

The isolated viral particle may be administered to the patient directly. For example, the isolated viral particle may be administered directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The isolated viral particle may be administered to the patient intrathecally, intravenously or via intracranial injection.

Alternatively, a cell may be infected with the isolated viral particle and the infected cell may be administered to the patient. The infected cell may be administered directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The infected cell may be administered to the patient intrathecally, intravenously or via intracranial injection.

According to still another aspect of the present disclosure, there is provided a method for inducing an immunogenic response in a patient, the method including administering an isolated viral particle according to the present disclosure to the patient.

The isolated viral particle may be administered to the patient directly. For example, the isolated viral particle may be administered directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The isolated viral particle may be administered to the patient intrathecally, intravenously or via intracranial injection.

Alternatively, a cell may be infected with the isolated viral particle and the infected cell may be administered to the patient. The infected cell may be administered directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The infected cell may be administered to the patient intrathecally, intravenously or via intracranial injection.

According to a yet further aspect of the present disclosure, there is provided a kit for the treatment of cancer in a patient, the kit including: the isolated viral particle according to any one of claims 1 to 12; and instructions for administration of the isolated viral particle to the patient.

The cancer may be a brain cancer. The brain cancer may be a glioblastoma.

The isolated viral particle may be formulated for direct delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The isolated viral particle may be formulated for administration via intrathecal, intravenous or intracranial injection.

Alternatively, the isolated viral particle may be formulated for infection of a cell where the cell is for delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. The cell may be for administration via intrathecal, intravenous or intracranial injection.

Other aspects and features of the present disclosure will become apparent to those ordinarily skilled in the art upon review of the following description of specific embodiments in conjunction with the accompanying figures.

BRIEF DESCRIPTION OF THE DRAWINGS

Embodiments of the present disclosure will now be described, by way of example only, with reference to the attached Figures.

FIG. 1A is a map showing the region FMT virus was isolated; FIG. 1B is a Amino Acid Blast alignment of 5 FMT putative open reading frames (ORFs) (N, P, G, M and L) reveals little sequence homology to known sequences in the NCBI database; FIG. 1C is a SDS PAGE gel of FMT virus showing 4 of the 5 predicted FMT ORF proteins; FIG. 1D is an illustration of the Phylogenic tree of various rhabdoviruses; FIG. 1E is an Example of a Fully replicative GFP expressing FMT strain; and FIG. 1F is an Electron microgram of FMT virion (adapted from Tesh et al. Emerging Infect. Dis. 2002).

FIG. 2A illustrates an intracranial neurotoxicity screen for rhabdoviruses; FIG. 2B is a graph illustrating motor function assessment by time on rotorod after intracerebral injection of FMT in Balb/C mice; FIG. 2C is a graph illustrating a FMT MTD determination in Balb/C mice injected IV with increasing doses (3xe6 pfu-3e9 pfu) of FMT virus; FIG. 2D is a table illustrating detection of viable FMT virus 3 months post-inoculation; FIG. 2E shows histopathology photographs of Brain following intracerebral inoculation with FMT. VSV or PBS.

FIG. 3A is a table showing a summary of FMT virus cytotoxicity in vitro; FIG. 3B is a set of graphs illustrating that FMT is a potent and selective killer of GBM cell lines; and FIG. 3C is a table showing an assessment of FMT potency against tumour and normal cells.

FIG. 4A is a set of photographs of a U-87 MG Human Glioma Xenograft Model; FIG. 4B is a graph illustrating a Kaplan Meier survival plot of animals treated with a single dose IC (1e5 pfu) or IV (5e8 pfu); FIG. 4C is a fluorescence micrograph of mock infected mouse brain (with GFP tagged U87MG tumour) versus FMT treated mouse brain; FIG. 4D is a graph illustrating a Late Syngeneic mouse GBM model using the CT2A cell line treated both IC and IV with FMT or PBS.

FIG. 5A is a photograph showing C57/B6 mice implanted with CT2A murine glioma cells into the striatum and treated with FMT and cured of initial tumour then challenged with CT2A cells implanted into the striatum versus Naive mice implanted with CT2A cells as a control; FIG. 5B is a graph illustrating C57/B6 mice implanted with CT2A murine glioma cells into the striatum and allowed to grow tumours received either anti-CD8 polyclonal serum injections to remove CD8+ T cells or matched pre-immune serum as a control then both groups were treated with a single intracranial dose of FMT to induce tumour regressions.

FIG. 6A is a photograph of a Western blot of human brain tumour cells (SNB19) and primary normal human astrocytes (NHA) showing FMT virus infection and protein production; FIG. 6B is a graph illustrating the growth curve of FMT virus production in SNB19 and NHA cells; FIG. 6C shows fluorescence microscopy photographs of GFP-expressing rec-FMT or Maraba-Δ51 virus added to a GM38 cell monolayer with and without treatment with the type I interferon inhibitor B18R protein derived from vaccinnia virus (VV-B18R); FIG. 6D is a graph illustrating plaque and infectious foci size measured from fluorescence microscopy; FIG. 6E is a graph illustrating an interferon bioassay in PC3 cells.

FIG. 7A is a graph illustrating viral titer determined in Teratocarcinoma and differentiated NT2 cells infected with the indicated viruses; FIG. 7B is a graph illustrating teratocarcinoma and differentiated NT2 cells infected with the indicated viruses and assayed for viability using Alamar blue metabolic dye; FIG. 7C shows photographs of Western blots of several components of the cellular apoptotic signaling cascade following infection of either tumour (SNB19 or normal cells (NHA); FIG. 7D is an illustration of a schematic of cellular apoptosis signaling cascade.

DESCRIPTION Definitions

Throughout the present disclosure, several terms are employed that are defined in the following paragraphs.

As used herein, the words “desire” or “desirable” refer to embodiments of the technology that afford certain benefits, under certain circumstances. However, other embodiments may also be desirable, under the same or other circumstances. Furthermore, the recitation of one or more desired embodiments does not imply that other embodiments are not useful, and is not intended to exclude other embodiments from the scope of the technology.

As used herein, the word “include,” and its variants, is intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the materials, compositions, devices, and methods of this technology. Similarly, the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features.

Although the open-ended term “comprising,” as a synonym of non-restrictive terms such as including, containing, or having, is used herein to describe and claim embodiments of the present technology, embodiments may alternatively be described using more limiting terms such as “consisting of” or “consisting essentially of.” Thus, for any given embodiment reciting materials, components or process steps, the present technology also specifically includes embodiments consisting of, or consisting essentially of, such materials, components or processes excluding additional materials, components or processes (for consisting of) and excluding additional materials, components or processes affecting the significant properties of the embodiment (for consisting essentially of), even though such additional materials, components or processes are not explicitly recited in this application. For example, recitation of a composition or process reciting elements A, B and C specifically envisions embodiments consisting of, and consisting essentially of, A, B and C, excluding an element D that may be recited in the art, even though element D is not explicitly described as being excluded herein.

As referred to herein, all compositional percentages are by weight of the total composition, unless otherwise specified. Disclosures of ranges are, unless specified otherwise, inclusive of endpoints and include all distinct values and further divided ranges within the entire range. Thus, for example, a range of “from A to B” or “from about A to about B” is inclusive of A and of B. Disclosure of values and ranges of values for specific parameters (such as temperatures, molecular weights, weight percentages, etc.) are not exclusive of other values and ranges of values useful herein. It is envisioned that two or more specific exemplified values for a given parameter may define endpoints for a range of values that may be claimed for the parameter. For example, if Parameter X is exemplified herein to have value A and also exemplified to have value Z, it is envisioned that Parameter X may have a range of values from about A to about Z. Similarly, it is envisioned that disclosure of two or more ranges of values for a parameter (whether such ranges are nested, overlapping or distinct) subsume all possible combination of ranges for the value that might be claimed using endpoints of the disclosed ranges. For example, if Parameter X is exemplified herein to have values in the range of 1-10, or 2-9, or 3-8, it is also envisioned that Parameter X may have other ranges of values including 1-9, 1-8, 1-3, 1-2, 2-10, 2-8, 2-3, 3-10, and 3-9.

“A” and “an” as used herein indicate “at least one” of the item is present; a plurality of such items may be present, when possible.

“About” when applied to values indicates that the calculation or the measurement allows some slight imprecision in the value (with some approach to exactness in the value; approximately or reasonably close to the value; nearly). If, for some reason, the imprecision provided by “about” is not otherwise understood in the art with this ordinary meaning, then “about” as used herein indicates at least variations that may arise from ordinary methods of measuring or using such parameters.

As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items.

As used herein, a virus that has “reduced levels of neurotoxicity” or “reduced neurotoxicity” would be understood to refer to a virus that, when injected into the right striatum of a mouse brain at a given dose, results in a mouse with fewer signs of neurotoxicity (for example, weigh loss, piloerection, hind leg paralysis, morbidity and mortality) than a mouse which is injected with wild-type maraba virus.

As used herein, “substantially no level of neurotoxicity” or “substantially no neurotoxicity” would be understood to refer to a virus that, when injected introcerebrally into a mouse at 1e6 pfu, results in a mouse with no detectable signs of reduced motor function as measured by time on a rotorod compared to the mouse before injection with the virus.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS

Of the more than 250 currently identified rhabdoviruses, several isolated wild type rhabdoviruses were determined to be effective at killing CNS tumour cell lines while retaining attenuation in normal human astrocytes and post-mitotic neurons. Several of these potent viral isolates were also determined to demonstrate remarkable attenuation, resulting in 100% survival after intracerebral inoculation. This is in striking contrast to previously tested Maraba and VSV viruses.

Generally, the present disclosure provides an oncolytic virus for the treatment of cancer. Oncolytic viruses may be used to treat cancer by directly administering the virus to a patient, or by infecting a cell with the virus and administering the infected cell to the patient to deliver the virus. The cell to be infected by the virus may be a cancer cell from the patient. In some examples, the cancer to be treated is brain cancer, such as malignant glioma. One example of a malignant glioma is glioblastoma. The oncolytic virus may exhibit reduced levels of neurotoxicity.

The oncolytic virus may be an isolated viral particle capable of producing a cDNA polynucleotide that includes a sequence according to SEQ ID NO: 1 when the virus is in a host cell.

The oncolytic virus may be an isolated viral particle that includes an RNA polynuclotide that includes a sequence according to SEQ ID NO: 2.

The oncolytic virus may be an isolated viral particle having a genome that includes open reading frames that encode: a protein having a sequence comprising SEQ ID NO: 3, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 4, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 5, or a variant thereof; a protein having a sequence comprising SEQ ID NO: 6, or a variant thereof; and a protein having a sequence comprising SEQ ID NO: 7, or a variant thereof.

The variant of a reference protein may be a protein that has a sequence which is at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the sequence of the reference protein, and where the variant protein maintains the same biological function as the reference protein.

In some examples, at least one of the open reading frames encodes a protein having a sequence which is a sequence selected from the group consisting of SEQ ID NOs: 3, 4, 5, 6, and 7. In such examples, the variant of a reference protein may be a protein having a sequence which is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the sequence of the reference protein, and where the variant protein maintains the same biological function as the reference protein.

The viral genome may include open reading frames that encode: a protein having a sequence comprising SEQ ID NO: 3; a protein having a sequence comprising SEQ ID NO: 4; a protein having a sequence comprising SEQ ID NO: 5; a protein having a sequence comprising SEQ ID NO: 6; and a protein having a sequence comprising SEQ ID NO: 7.

The isolated viral particle may further include at least one additional open reading frame for encoding at least one additional protein. The additional protein may be an immunogenic protein.

The oncolytic virus may be an isolated viral particle capable of producing a cDNA polynucleotide when the virus is in a host cell, the cDNA polynucleotide having a sequence that includes: SEQ ID NO: 8, or a conservative variant thereof; SEQ ID NO: 9, or a conservative variant thereof; 2894-3340 of SEQ ID NO: 10, or a conservative variant thereof; SEQ ID NO: 11, or a conservative variant thereof; SEQ ID NO: 12, or a conservative variant thereof; and promoters thereof.

The conservative variant of a sequence of nucleotides may be a sequence that is at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to the reference sequence of nucleotides. The conservative variant may be a sequence comprising one or more silent substitutions.

An isolated viral particle according to the present disclosure may be used for the treatment of cancer. The cancer may be a brain cancer. The brain cancer may be a glioblastoma. The isolated viral particle may be used for the treatment of cancer by infecting a cell with the virus and the infected cell may be used to deliver the virus to a patient. Techniques for infecting a cell with a virus and using the infected cell to deliver the virus are discussed in, for example: Power A T, et al. Carrier cell-based delivery of an oncolytic virus circumvents antiviral immunity. Mol Ther. 2007 January; 15(1):123-30; and Tyler M A, et al. Neural stem cells target intracranial glioma to deliver an oncolytic adenovirus in vivo. Gene Ther. 2009 February; 16(4262-78.

An isolated viral particle according to the present disclosure may be used to induce an immunogenic response in a person administered the virus. The immunogenic response may be an anti-cancer response. The isolated viral particle may be used induce an immunogenic response by infecting a cell with the virus and the infected cell may be used to deliver the virus to the person.

The isolated viral particle may be formulated for direct delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. For example the isolated viral particle may be formulated for administration via intrathecal, intravenous or intracranial injection.

An isolated viral particle according to the present disclosure may be used in a a method for treating cancer, where the method includes administering an isolated viral particle according the present disclosure to a patient having cancer. The cancer may be a brain cancer. The brain cancer may be a glioblastoma. The isolated viral particle may be administered to the patient directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. For example, the isolated viral particle may be administered intrathecally, intravenously or via intracranial injection. The isolated viral particle may be directly administered to the patient or may be administered to the patient by infecting a cell with the virus and administering the infected cell to the patient.

An isolated viral particle according to the present disclosure may be used in a method for inducing an immunogenic response in a patient, where the method includes administering an isolated viral particle according to the present disclosure to the patient. The isolated viral particle may be administered to the patient directly to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. For example, the isolated viral particle may be administered intrathecally, intravenously or via intracranial injection.

An isolated viral particle according to the present disclosure may be included in a kit for the treatment of cancer in a patient, the kit including: the isolated viral particle according to the present disclosure; and instructions for administration of the isolated viral particle to the patient. The cancer may be a brain cancer. The brain cancer may be a glioblastoma. The isolated viral particle may be formulated for direct delivery to the central nervous system, outside the blood/brain barrier, inside the blood/brain barrier, or any combination thereof. For example the isolated viral particle may be formulated for administration via intrathecal, intravenous or intracranial injection.

One example of a rhabdovirus that was determined to be effective at killing CNS tumour cell lines while retaining attenuation in normal human astrocytes and post-mitotic neurons was Farmington rhabdovirus (FMT). See Example 1 and FIG. 1 for a discussion of the genetic components of FMT. Interestingly, FMT shows little or no sequence homology to other rhabdoviruses from the six current genera and thus may constitute a seventh genus in the Rhabdoviridae. This virus was determined to exhibit reduced neurotoxicity after intracranial administration (see Example 2 and FIG. 2). The FMT virus also demonstrated tumour selectivity in vitro (see Example 3 and FIG. 3), and safety and efficacy following intracranial or systemic administration in syngeneic and xenograft mouse models of glioblastoma (see Example 4 and FIG. 4).

As discussed above, several viruses, including Maraba (MRB), Farmington (FMT) and Carajas (CRJ), were determined to have potent killing capacity against a variety of cancer cell lines from the NC60 cell panel. These viruses were also determined to have an ability to eradicate CNS tumour cell lines. These viruses were tested for their safety and efficacy in vitro and in vivo.

Previous viruses, such as wild type and attenuated strains of VSV, are also known to be potent killers of CNS cell lines. However, they are notably neurotoxic and treatment with such viruses often results in rapid weight loss and paralysis upon intracerebral injection at very low doses. Such neurotoxicity prevents application of VSV to treating brain cancer.

As illustrated in Example 2 and FIG. 2, it was determined that, like VSV, both CRJ and MRB also resulted in neurotoxicity in Balb/C mice within a period of 2-7 days after administration. However, it was surprisingly determined that FMT demonstrated no neurotoxicity up to 30 days following direct intracranial injection (IC) of 1e6 pfu.

FMT was determined to be able to kill GBM cells at low multiplicities of infection, and was determined to possess replication kinetics and large burst sizes that rivaled those of the highly lytic Maraba virus. FMT was also determined to be poorly cytolytic in normal human astrocytes and primary neurons (see Example 3 and FIG. 3). The mechanism of tumour selectivity appears to be independent of interferon signaling, as is currently the established mechanism of selectivity governing rhabdovirus based oncolytic agents. FMT appears to infect normal cells equally to tumour cells, but only induces apoptosis in tumour cells. FMT was determined to not trigger caspase 8 in normal cells, even though there is robust virus protein synthesis. Moreover. FMT's selective cytotoxicity mechanism rendered the virus non-neurotoxic despite its strong ability to block interferon (IFN) production. This indicates that rhabdovirus infections of the CNS cannot be effectively controlled by interferon anti-virus defenses when viruses are delivered directly into the brain. When delivered peripherally. FMT was determined to be as attenuated as previously published engineered VSV deltaM51 or MR MG1 strains.

As illustrated in Example 4 and FIG. 4, the FMT virus may be used to treat human xenograft and immunocompetent syngeneic models by either local regional or systemic administration. In vivo efficacy in a human orthotopic U87MG model after a single IC or IV dose of FMT is described in Example 4. In fact, IV even achieved durable cures. Notably both modes of delivery are not only able to treat the primary glioma but are able to effectively and durably treat U87MG spinal metastasis in 100% of the animals. Based on these results, it is expected that FMT virus could be used to treat other cancers, such as, for example, medulloblastomas. It is expected that FMT virus could be used to treat primary cancers as well as metastasized cancers, such as to the CNS. Although FMT virus exhibits reduced neurotoxicity and is, for that reason, suitable for use in the treatment of neurological tumors, it should be understood that the FMT virus may be used for the treatment of non-neurological cancers. It should also be understood that other viruses according to the present disclosure could be used for the treatment of non-neurological cancers.

FMT virus has been demonstrated to induce an anti-tumor immunity. As illustrated in Example 5 and FIG. 5, mice previously harboring CT-2A tumors that had been successfully treated with IC FMT virus infusions were injected for a second time with CT-2A cells directly into the brain. It was determined that previously cured mice rejected the cells. When, concomitant with FMT virus treatment, cytotoxic T-lymphocytes (CTL) were removed using antibodies directed toward CD8, it was determined that mice stripped of their CD8+ T-cells all eventually re-grew the subsequently injected CT-2A cells and failed therapy. This suggests that in addition to direct tumour cell lysis and putative other mechanisms of action, the FMT virus induces an anti-tumor immunity when CTLs are present. Accordingly, it is expected that a virus according to the present disclosure may be used to induce an immune response in a patient exposed to the virus. The immune response may be, for example, an anti-cancer immune response.

Several groups have also shown impressive efficacy in U87MG model but seldom in a syngeneic immunocompetent GBM model. Moreover, GBM models are often treated at predetermined times when animals are still healthy and tumours presumably small. In the examples discussed herein, treatment was commenced 14 days post implantation, which is approximately 4-7 days before the animals displayed symptoms of their disease. In the orthoptopic CT-2A syngeneic GBM model, treatment was commenced at a stage (19 days post implantation) when animals started displaying overt symptoms of disease. These symptoms include lack of grooming, hydrocephaly, and hunched phenotype. This treatment protocol is believed to be particularly relevant to the clinical setting where patients are diagnosed and treated after presenting with symptoms. In the examples discussed herein, either a single IC dose or 6 IV doses of FMT was administered. The results demonstrated a similarly significant survival profile achieving a significant prolongation in survival and several mice in each group (20-30%) were durably cured beyond 100 days. The CT-2A model was chosen because it resulted in an aggressive infiltrative tumour and shares proliferative, metabolic, histological, and immunohistochemical profiles observed in human glioblastoma multiforme.

The FMT virus was also demonstrated to not distinguish tumor from non-tumor cells via differential infectivity or viral protein production (see Example 6 and FIG. 6). The FMT virus is similarly productive in non-cancerous as compared to cancerous cells. Example 6 also demonstrated that the genome of wild type FMT virus may be mutated to include an additional protein, in the present example the additional protein added to the genome of wild type FMT virus was green fluorescent protein (GFP). The resulting mutated “rec-FMT-GFP virus” was demonstrated to block human type I interferon response and productively infect both cancerous and non-cancerous cells.

The FMT virus was also demonstrated to induce cell death in a manner dependent on the anti-apoptotic threshold of the infected cells, and not on the productivity of the virus infection within the infected cell (see Example 7 and FIG. 7). FMT viral infection of a cell appears to initiate activation (cleavage) of caspase 8, caspase 9. BH3-interacting domain and Poly(ADP-ribose) Polymerase in tumor cells.

In summary, FMT is an exemplary oncolytic virus according to the present disclosure, and which has been demonstrated to have a high therapeutic index against human brain cancer cell lines and patient samples in vitro, and which has a demonstrated potent efficacy when used to treat preclinical models of brain cancer. Accordingly, it is expected that isolated viral particles according to the present disclosure may be used to treat cancer, such as brain cancer (for example glioblastoma). It is also expected that isolated viral particles according to the present disclosure may be used to induce an immunogenic response, such as an anti-cancer response, in a person administered the virus.

Polynucleotide and Amino Acid Sequences

Polynucleotides comprising nucleic acid sequences (e.g., DNA and RNA) and amino acid (e.g., protein) sequences are provided that may be used in a variety of methods and techniques known to those skilled in the art of molecular biology. These include isolated, purified, and recombinant forms of the listed sequences and further include complete or partial forms of the listed sequences. Non-limiting uses for amino acid sequences include making antibodies to proteins or peptides comprising the disclosed amino acid sequences. Non-limiting uses for the polynucleotide sequences include making hybridization probes, as primers for use in the polymerase chain reaction (PCR), for chromosome and gene mapping, and the like. Complete or partial amino acid or polynucleotide sequences can be used in such methods and techniques.

The present disclosure features the identification of polynucleotide sequences, including gene sequences and coding nucleic acid sequences, and amino acid sequences. In addition to the sequences expressly provided in the accompanying sequence listing, also included are polynucleotide sequences that are related structurally and/or functionally. Also included are polynucleotide sequences that hybridize under stringent conditions to any of the polynucleotide sequences in the sequence listing, or a subsequence thereof (e.g., a subsequence comprising at least 100 contiguous nucleotides). Polynucleotide sequences also include sequences and/or subsequences configured for RNA production and/or translation, e.g., mRNA, antisense RNA, sense RNA, RNA silencing and interference configurations, etc.

Polynucleotide sequences that are substantially identical to those provided in the sequence listing can be used in the compositions and methods disclosed herein. Substantially identical or substantially similar polynucleotide sequences are defined as polynucleotide sequences that are identical, on a nucleotide by nucleotide basis, with at least a subsequence of a reference polynucleotide. Such polynucleotides can include, e.g., insertions, deletions, and substitutions relative to any of those listed in the sequence listing. For example, such polynucleotides are typically at least about 70% identical to a reference polynucleotide selected from those in the sequence listing, or a subsequence thereof. For example, at least 7 out of 10 nucleotides within a window of comparison are identical to the reference sequence selected. Furthermore, such sequences can be at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or at least about 99.5%, identical to the reference sequence. Subsequences of these polynucleotides can include at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 50, at least about 75, at least about 100, at least about 500, about 1000 or more, contiguous nucleotides or complementary subsequences. Such subsequences can be, e.g., oligonucleotides, such as synthetic oligonucleotides, isolated oligonucleotides, or full-length genes or cDNAs. Polynucleotide sequences complementary to any of the described sequences are included.

Amino acid sequences include the amino acid sequences represented in the sequence listing, and subsequences thereof. Also included are amino acid sequences that are highly related structurally and/or functionally. For example, in addition to the amino acid sequences in the sequence listing, amino acid sequences that are substantially identical can be used in the disclosed compositions and methods. Substantially identical or substantially similar amino acid sequences are defined as amino acid sequences that are identical, on an amino acid by amino acid basis, with at least a subsequence of a reference amino acid sequence. Such amino acid sequences can include, e.g., insertions, deletions, and substitutions relative to any of the amino acid sequences in the sequence listing. For example, such amino acids are typically at least about 70% identical to a reference amino acid sequence, or a subsequence thereof. For example, at least 7 out of 10 amino acids within a window of comparison are identical to the reference amino acid sequence selected. Frequently, such amino acid sequences are at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or at least about 99.5%, identical to the reference sequence. Subsequences of the amino acid sequences can include at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 50, at least about 75, at least about 100, at least about 500, about 1000 or more, contiguous amino acids. Conservative variants of amino acid sequences or subsequences are also possible. Amino acid sequences can be immunogenic, enzymatically active, enzymatically inactive, and the like.

Where the polynucleotide sequences are translated to form a polypeptide or subsequence of a polypeptide, nucleotide changes can result in either conservative or non-conservative amino acid substitutions. Conservative amino acid substitutions refer to the interchangeability of residues having functionally similar side chains. Conservative substitution tables providing functionally similar amino acids are well known in the art. Table 1 sets forth examples of six groups containing amino acids that are “conservative substitutions” for one another. Other conservative substitution charts are available in the art, and can be used in a similar manner.

TABLE 1 Conservative Substitution Group 1 Alanine (A) Serine (S) Threonine (T) 2 Aspartic acid (D) Glutamic acid (E) 3 Asparagine (N) Glutamine (Q) 4 Arginine (R) Lysine (K) 5 Isoleucine (I) Leucine (L) Methionine (M) Valine (V) 6 Phenylalanine (F) Tyrosine (Y) Tryptophan (W)

One of skill in the art will appreciate that many conservative substitutions yield functionally identical constructs. For example, as discussed above, owing to the degeneracy of the genetic code, “silent substitutions” (i.e., substitutions in a polynucleotide sequence which do not result in an alteration in an encoded polypeptide) are an implied feature of every polynucleotide sequence which encodes an amino acid. Similarly, “conservative amino acid substitutions,” in one or a few amino acids in an amino acid sequence (e.g., about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10% or more) are substituted with different amino acids with highly similar properties, are also readily identified as being highly similar to a disclosed construct. Such conservative variations of each disclosed sequence are also contemplated.

Methods for obtaining conservative variants, as well as more divergent versions of the polynucleotide and amino acid sequences, are widely known in the art. In addition to naturally occurring homologues which can be obtained, e.g., by screening genomic or expression libraries according to any of a variety of well-established protocols, see, e.g., Ausubel et al. Current Protocols in Molecular Biology (supplemented through 2004) John Wiley & Sons, New York (“Ausubel”); Sambrook et al. Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”), and Berger and Kimmel Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”), additional variants can be produced by any of a variety of mutagenesis procedures. Many such procedures are known in the art, including site directed mutagenesis, oligonucleotide-directed mutagenesis, and many others. For example, site directed mutagenesis is described, e.g., in Smith (1985) “In vitro mutagenesis” Ann. Rev. Genet. 19:423-462, and references therein, Botstein & Shortle (1985) “Strategies and applications of in vitro mutagenesis” Science 229:1193-1201; and Carter (1986) “Site-directed mutagenesis” Biochem. J. 237:1-7. Oligonucleotide-directed mutagenesis is described, e.g., in Zoller & Smith (1982) “Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any DNA fragment” Nucleic Acids Res. 10:6487-6500). Mutagenesis using modified bases is described e.g., in Kunkel (1985) “Rapid and efficient site-specific mutagenesis without phenotypic selection” Proc. Natl. Acad. Sci. USA 82:488-492, and Taylor et al. (1985) “The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA” Nucl. Acids Res. 13: 8765-8787. Mutagenesis using gapped duplex DNA is described, e.g., in Kramer et al. (1984) “The gapped duplex DNA approach to oligonucleotide-directed mutation construction” Nucl. Acids Res. 12: 9441-9460). Point mismatch mutagenesis is described, e.g., by Kramer et al. (1984) “Point Mismatch Repair” Cell 38:879-887). Double-strand break mutagenesis is described, e.g., in Mandecki (1986) “Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis” Proc. Natl. Acad. Sci. USA, 83:7177-7181, and in Arnold (1993) “Protein engineering for unusual environments” Current Opinion in Biotechnology 4:450-455). Mutagenesis using repair-deficient host strains is described, e.g., in Carter et al. (1985) “Improved oligonucleotide site-directed mutagenesis using M13 vectors” Nucl. Acids Res. 13: 4431-4443. Mutagenesis by total gene synthesis is described e.g., by Nambiar et al. (1984) “Total synthesis and cloning of a gene coding for the ribonuclease S protein” Science 223: 1299-1301. DNA shuffling is described, e.g., by Stemmer (1994) “Rapid evolution of a protein in vitro by DNA shuffling” Nature 370:389-391, and Stemmer (1994) “DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution,” Proc. Natl. Acad. Sci. USA 91:10747-10751.

Many of the above methods are further described in Methods in Enzymology Volume 154, which also describes useful controls for trouble-shooting problems with various mutagenesis methods. Kits for mutagenesis, library construction and other diversity generation methods are also commercially available. For example, kits are available from, e.g., Amersham International plc (Piscataway, N.J.) (e.g., using the Eckstein method above), Bio/Can Scientific (Mississauga, Ontario, CANADA), Bio-Rad (Hercules, Calif.) (e.g., using the Kunkel method described above), Boehringer Mannheim Corp. (Ridgefield, Conn.), Clonetech Laboratories of BD Biosciences (Palo Alto, Calif.), DNA Technologies (Gaithersburg, Md.), Epicentre Technologies (Madison, Wis.) (e.g., the 5 prime 3 prime kit); Genpak Inc. (Stony Brook, N.Y.), Lemargo Inc (Toronto, CANADA), Invitrogen Life Technologies (Carlsbad, Calif.), New England Biolabs (Beverly, Mass.), Pharmacia Biotech (Peapack, N.J.), Promega Corp. (Madison, Wis.), QBiogene (Carlsbad, Calif.), and Stratagene (La Jolla, Calif.) (e.g., QuickChange™ site-directed mutagenesis kit and Chameleon™ double-stranded, site-directed mutagenesis kit).

Determining Sequence Relationships

Similar sequences can be objectively determined by any number of methods, e.g., percent identity, hybridization, immunologically, and the like. A variety of methods for determining relationships between two or more sequences (e.g., identity, similarity and/or homology) are available and well known in the art. Methods include manual alignment, computer assisted sequence alignment, and combinations thereof, for example. A number of algorithms (which are generally computer implemented) for performing sequence alignment are widely available or can be produced by one of skill. These methods include, e.g., the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443; the search for similarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. (USA) 85:2444; and/or by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).

For example, software for performing sequence identity (and sequence similarity) analysis using the BLAST algorithm is described in Altschul et al. (1990) J. Mol. Biol. 215:403-410. This software is publicly available, e.g., through the National Center for Biotechnology Information on the Internet at ncbi.nlm.nih.gov. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP (BLAST Protein) program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see, Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

Additionally, the BLAST algorithm performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul (1993) Proc. Nat'l. Acad. Sci. USA 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (p(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence (and, therefore, in this context, homologous) if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, or less than about 0.01, and or even less than about 0.001.

Another example of a sequence alignment algorithm is PILEUP, which creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle (1987) J. Mol. Evol. 35:351-360. The method used is similar to the method described by Higgins & Sharp (1989) CABIOS5:151-153. The program can align, e.g., up to 300 sequences of a maximum length of 5,000 letters. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster can then be aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences can be aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program can also be used to plot a dendogram or tree representation of clustering relationships. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison.

An additional example of an algorithm that is suitable for multiple DNA, or amino acid, sequence alignments is the CLUSTALW program (Thompson, J. D. et al. (1994) Nucl. Acids. Res. 22: 4673-4680). CLUSTALW performs multiple pairwise comparisons between groups of sequences and assembles them into a multiple alignment based on homology. Gap open and Gap extension penalties can be, e.g., 10 and 0.05 respectively. For amino acid alignments, the BLOSUM algorithm can be used as a protein weight matrix. See, e.g., Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915-10919.

Polynucleotide hybridization similarity can also be evaluated by hybridization between single stranded (or single stranded regions of) nucleic acids with complementary or partially complementary polynucleotide sequences. Hybridization is a measure of the physical association between nucleic acids, typically, in solution, or with one of the nucleic acid strands immobilized on a solid support, e.g., a membrane, a bead, a chip, a filter, etc. Nucleic acid hybridization occurs based on a variety of well characterized physico-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking, and the like. Numerous protocols for nucleic acid hybridization are well known in the art. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, part I, chapter 2, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” (Elsevier. N.Y.), as well as in Ausubel et al. Current Protocols in Molecular Biology (supplemented through 2004) John Wiley & Sons, New York (“Ausubel”); Sambrook et al. Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”), and Berger and Kimmel Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”). Hames and Higgins (1995) Gene Probes 1, IRL Press at Oxford University Press, Oxford, England (Hames and Higgins 1) and Hames and Higgins (1995) Gene Probes 2, IRL Press at Oxford University Press, Oxford, England (Hames and Higgins 2) provide details on the synthesis, labeling, detection and quantification of DNA and RNA, including oligonucleotides.

Conditions suitable for obtaining hybridization, including differential hybridization, are selected according to the theoretical melting temperature (Tm) between complementary and partially complementary nucleic acids. Under a given set of conditions, e.g., solvent composition, ionic strength, etc., the. Tm is the temperature at which the duplex between the hybridizing nucleic acid strands is 50% denatured. That is, the Tm corresponds to the temperature corresponding to the midpoint in transition from helix to random coil; it depends on the length of the polynucleotides, nucleotide composition, and ionic strength, for long stretches of nucleotides.

After hybridization, unhybridized nucleic acids can be removed by a series of washes, the stringency of which can be adjusted depending upon the desired results. Low stringency washing conditions (e.g., using higher salt and lower temperature) increase sensitivity, but can product nonspecific hybridization signals and high background signals. Higher stringency conditions (e.g., using lower salt and higher temperature that is closer to the T.sub.m) lower the background signal, typically with primarily the specific signal remaining, See, also, Rapley, R. and Walker, J. M. eds., Molecular Biomethods Handbook (Humana Press, Inc. 1998).

“Stringent hybridization wash conditions” or “stringent conditions” in the context of nucleic acid hybridization experiments, such as Southern and northern hybridizations, are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993), supra, and in Hames and Higgins 1 and Hames and Higgins 2, supra.

An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 2×SSC, 50% formamide at 42° C., with the hybridization being carried out overnight (e.g., for approximately 20 hours). An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see Sambrook, supra for a description of SSC buffer). Often, the wash determining the stringency is preceded by a low stringency wash to remove signal due to residual unhybridized probe. An example low stringency wash is 2×SSC at room temperature (e.g., 20° C. for 15 minutes).

In general, a signal to noise ratio of at least 2.5×−5× (and typically higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Detection of at least stringent hybridization between two sequences indicates relatively strong structural similarity to those provided in the sequence listings herein.

Generally, “highly stringent” hybridization and wash conditions are selected to be about 5° C. or less lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH (as noted below, highly stringent conditions can also be referred to in comparative terms). Target sequences that are closely related or identical to the nucleotide sequence of interest (e.g., “probe”) can be identified under stringent or highly stringent conditions. Lower stringency conditions are appropriate for sequences that are less complementary.

For example, in determining stringent or highly stringent hybridization (or even more stringent hybridization) and wash conditions, the stringency of the hybridization and wash conditions is gradually increased (e.g., by increasing temperature, decreasing salt concentration, increasing detergent concentration, and/or increasing the concentration of organic solvents, such as formamide, in the hybridization or wash), until a selected set of criteria are met. For example, the stringency of the hybridization and wash conditions is gradually increased until a probe comprising one or more of the present polynucleotide sequences, or a subsequence thereof, and/or complementary polynucleotide sequences thereof, binds to a perfectly matched complementary target, with a signal to noise ratio that is at least 2.5×, and optionally 5×, or 10×, or 100× or more, as high as that observed for hybridization of the probe to an unmatched target, as desired.

Using subsequences derived from the nucleic acids listed in the sequence listing, novel target nucleic acids can be obtained; such target nucleic acids are also a feature of the invention. For example, such target nucleic acids include sequences that hybridize under stringent conditions to an oligonucleotide probe that corresponds to a unique subsequence of any of the polynucleotides in the sequence listing, or a complementary sequence thereof; the probe optionally encodes a unique subsequence in any of the amino acid sequences of the sequence listing.

For example, hybridization conditions are chosen under which a target oligonucleotide that is perfectly complementary to the oligonucleotide probe hybridizes to the probe with at least about a 5-10× higher signal to noise ratio than for hybridization of the target oligonucleotide to a negative control non-complimentary nucleic acid. Higher ratios of signal to noise can be achieved by increasing the stringency of the hybridization conditions such that ratios of about 15×, 20×, 30×, 50× or more are obtained. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a calorimetric label, a radioactive label, or the like.

Vectors, Promoters and Expression Systems

Polynucleotide sequences of the present disclosure can be in any of a variety of forms, e.g., expression cassettes, vectors, plasmids, viral particles, or linear nucleic acid sequences. For example, vectors, plasmids, cosmids, bacterial artificial chromosomes (BACs), YACs (yeast artificial chromosomes), phage, viruses and nucleic acid segments can comprise the present nucleic acid sequences or subsequences thereof. These nucleic acid constructs can further include promoters, enhancers, polylinkers, regulatory genes, etc. Thus, the present disclosure also relates, e.g., to vectors comprising the polynucleotides disclosed herein, host cells that incorporate these vectors, and the production of the various disclosed polypeptides (including those in the sequence listing) by recombinant techniques.

In accordance with these aspects, the vector may be, for example, a plasmid vector, a single or double-stranded phage vector, or a single or double-stranded RNA or DNA viral vector. Such vectors may be introduced into cells as polynucleotides, preferably DNA, by well known techniques for introducing DNA and RNA into cells. The vectors, in the case of phage and viral vectors, also may be and preferably are introduced into cells as packaged or encapsidated virus by well known techniques for infection and transduction. Viral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.

In some examples, vectors include those useful for expression of polynucleotides and polypeptides of the present invention. Generally, such vectors comprise cis-acting control regions effective for expression in a host, operably linked to the polynucleotide to be expressed. Appropriate trans-acting factors are supplied by the host, supplied by a complementing vector or supplied by the vector itself upon introduction into the host.

In certain examples in this regard, the vectors provide for protein expression. Such preferred expression may be inducible expression, temporally limited expression, or expression restricted to predominantly certain types of cells, or any combination of the above. Some embodiments of inducible vectors can be induced for expression by environmental factors that are easy to manipulate, such as temperature and nutrient additives. A variety of vectors suitable to this aspect, including constitutive and inducible expression vectors for use in prokaryotic and eukaryotic hosts, are well known and employed routinely by those of skill in the art. Such vectors include, among others, chromosomal, episomal and virus-derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as rhabdoviruses, baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids and binaries used for Agrobacterium-mediated transformations.

Vectors can include a selectable marker and a reporter gene. For ease of obtaining sufficient quantities of vector, a bacterial origin that allows replication in E. coli can be used. The following vectors, which are commercially available, are provided by way of example. Among vectors preferred for use in bacteria are pQE70, pQE60 and pQE-9, available from Qiagen; pBS vectors, Phagescript vectors, Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available from Stratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Useful plant binary vectors include BIN19 and its derivatives available from Clontech. These vectors are listed solely by way of illustration of the many commercially available and well-known vectors that are available to those of skill in the art. It will be appreciated that any other plasmid or vector suitable for, for example, introduction, maintenance, propagation or expression of one or more polynucleotides and/or polypeptides as provided in the present sequence listing, including variants thereof as described, in a host may be used.

In general, expression constructs will contain sites for transcription initiation and termination, and, in the transcribed region, a ribosome-binding site for translation when the construct encodes a polypeptide. The coding portion of the mature transcripts expressed by the constructs will include a translation-initiating AUG at the beginning and a termination codon appropriately positioned at the end of the polypeptide to be translated. In addition, the constructs may contain control regions that regulate as well as engender expression. Generally, in accordance with many commonly practiced procedures, such regions will operate by controlling transcription, such as transcription factors, repressor binding sites and termination signals, among others. For secretion of a translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incorporated into the expressed polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.

Transcription of the DNA (e.g., encoding the polypeptides) of the present invention by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp that act to increase transcriptional activity of a promoter in a given host cell-type. Examples of enhancers include the SV40 enhancer, which is located on the late side of the replication origin at bp 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. Additional enhancers useful in the invention to increase transcription of the introduced DNA segment, include, inter alia, viral enhancers like those within the 35S promoter, as shown by Odell et al., Plant Mol. Biol. 10:263-72 (1988), and an enhancer from an opine gene as described by Fromm et al., Plant Cell 1:977 (1989). The enhancer may affect the tissue-specificity and/or temporal specificity of expression of sequences included in the vector.

Termination regions also facilitate effective expression by ending transcription at appropriate points. Useful terminators include, but are not limited to, pinII (see An et al., Plant Cell 1(1):115-122 (1989)), glb1 (see Genbank Accession #L22345), gz (see gzw64a terminator, Genbank Accession #S78780), and the nos terminator from Agrobacterium. The termination region can be native with the promoter nucleotide sequence, can be native with the DNA sequence of interest, or can be derived from another source. For example, other convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also: Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. 1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.

Among known eukaryotic promoters suitable for generalized expression are the CMV immediate early promoter, the HSV thymidine kinase promoter, the early and late SV40 promoters, the promoters of retroviral LTRs, such as those of the Rous sarcoma virus (“RSV”), metallothionein promoters, such as the mouse metallothionein-I promoter and various plant promoters, such as globulin-1. The native promoters of the polynucleotide sequences listing in the sequence listing may also be used. Representatives of prokaryotic promoters include the phage lambda PL promoter, the E. coli lac, trp and tac promoters to name just a few of the well-known promoters.

Isolated or recombinant viruses, virus infected cells, or cells including one or more portions of the present polynucleotide sequences and/or expressing one or more portions of the present amino acid sequences are also contemplated.

A polynucleotide, optionally encoding the heterologous structural sequence of an amino acid sequence as disclosed, generally will be inserted into a vector using standard techniques so that it is operably linked to a promoter for expression. Operably linked, as used herein, includes reference to a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA corresponding to the second sequence. Generally, operably linked means that the polynucleotide sequence being linked is contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. When the polynucleotide is intended for expression of a polypeptide, the polynucleotide will be positioned so that the transcription start site is located appropriately 5′ to a ribosome binding site. The ribosome-binding site will be 5′ to the AUG that initiates translation of the polypeptide to be expressed. Generally, there will be no other open reading frames that begin with an initiation codon, usually AUG, and lie between the ribosome binding site and the initiation codon. Also, generally, there will be a translation stop codon at the end of the polypeptide and there will be a polyadenylation signal in constructs for use in eukaryotic hosts. Transcription termination signals appropriately disposed at the 3′ end of the transcribed region may also be included in the polynucleotide construct.

For nucleic acid constructs designed to express a polypeptide, the expression cassettes can additionally contain 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picornavirus leaders, for example: EMCV leader (Encephalomyocarditis 5′ noncoding region). Elroy-Stein et al. (1989) Proc. Nat. Acad. Sci. USA 86:6126-6130; potyvirus leaders, for example, TEV leader (Tobacco Etch Virus), Allison et al. (1986); MDMV leader (Maize Dwarf Mosaic Virus), Virology 154:9-20; human immunoglobulin heavy-chain binding protein (BiP). Macejak et al. (1991) Nature 353:90-94; untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4), Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV), Gallie et al. (1989) Molecular Biology of RNA, pages 237-256; and maize chlorotic mottle virus leader (MCMV) Lommel et al. (1991) Virology 81:382-385. See also Della-Cioppa et al. (1987) Plant Physiology 84:965-968. The cassette can also contain sequences that enhance translation and/or mRNA stability such as introns. The expression cassette can also include, at the 3′ terminus of the isolated nucleotide sequence of interest, a translational termination region.

In those instances where it is desirable to have the expressed product of the polynucleotide sequence directed to a particular organelle or secreted at the cell's surface the expression cassette can further comprise a coding sequence for a transit peptide. Such transit peptides are well known in the art and include, but are not limited to: the transit peptide for the acyl carrier protein, the small subunit of RUBISCO, plant EPSP synthase, and the like.

In making an expression cassette, the various DNA fragments can be manipulated so as to provide for the polynucleotide sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers can be employed to join DNA fragments or other manipulations can be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction digests, annealing, and resubstitutions such as transitions and transversions, can be employed.

Introduction of a construct into a host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction, infection or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods in Molecular Biology, (1986) and Sambrook et al., Molecular Cloning—A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).

Representative examples of appropriate hosts include bacterial cells, such as streptococci, staphylococci. E. coli, streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS and Bowes melanoma cells; and plant cells.

The host cells can be cultured in conventional nutrient media, which may be modified as appropriate for, inter alia, activating promoters, selecting transformants or amplifying genes. Culture conditions, such as temperature, pH and the like, previously used with the host cell selected for expression generally will be suitable for expression of nucleic acids and/or polypeptides, as will be apparent to those of skill in the art. Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the polynucleotides disclosed herein.

Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, where the selected promoter is inducible it is induced by appropriate means (e.g., temperature shift or exposure to chemical inducer) and cells are cultured for an additional period. Cells typically then are harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents; such methods are well known to those skilled in the art.

Compositions and methods of the present disclosure can include administering the polynucleotides and/or amino acids as provided herein. For example, treatments for glioblastoma can include administering one or more of the polynucleotides and/or amino acids. The one or more polynucleotides and/or amino acids may be in an isolated form or may be part of a composition, including a viral particle. In various embodiments, the administering can take the following forms: intradermal, transdermal, parenteral, intravascular, intravenous, intramuscular, intranasal, subcutaneous, regional, percutaneous, intratracheal, intraperitoneal, intraarterial, intravesical, intratumoral, inhalation, perfusion, lavage, direct injection, alimentary, oral, or intracranial administration.

Materials and Methods

Cell lines: U87MG, U343, U373, SF268, SF265, SF539, SNB19, SNB75, Vero, U118, normal human astrocytes (NHA), CT-2A, DBT, GL261 and human GM38 primary fibroblasts (National Institute of General Medical Sciences Mutant Cell Repository, Camden, N.J.) were propagated in Dulbeccos modified Eagle's medium (Hyclone, Logan, Utah) supplemented with 10% fetal calf serum (Cansera, Etobicoke, Ontario, Canada).

Viability Assays: The indicated cell lines were plated at a density of 10 000 cells/well into 96 well plates. The next day cells were infected with the rMarabaWT, or FMT at various multiplicity of infections (0.0001-10 pfu/cell). Following a 48 hour incubation Alamar Blue (Resazurin sodium salt (Sigma-Aldrich)) was added to a final concentration of 20 μg/ml. After a 6 hour incubation the absorbance was read at a wavelength of 573 nm.

Plaque assays: Vero cells were plated at a density of 5e5 cells per/well of a 6 well dish. The next day 100 l of serial viral dilutions were prepared and added for 1 hour to Vero cells. After viral adsorption 2 ml of agarose overlay was added (1:1 1% agarose:2×DMEM and 20% FCS). Plaques were counted the following day.

Interferon bioassay: PC-3 cells were infected with rMarabaWT. ΔM51 or FMT, at a multiplicity of infection of 3 pfu/cell for 24 hours. The following day supernatant was acid neutralized with 0.25N HCl overnight at 4° C. followed by the addition of 0.25 NaOH to adjust the pH to 7. Vero cells were incubated with the neutralized supernatant for 24 hours and subsequently infected rMaraba WT with a multiplicity of infection ranging from 0.0001 to 100 pfu/cell. Any interferon secreted by the PC-3 cells in response to Maraba or the attenuated mutants would subsequently protect the Vero cells from infection with Maraba. After 24 hours, survival was quantitated using a crystal violet assay. Briefly cells were incubated with 1% crystal violet solution, washed, dried, resuspended in 1% SDS and read at a wavelength of 595 nm.

Determination of in vivo toxicity: For the intracranial (IC) route of administration (roa), groups of 6-8 week old female BALB/c mice (n=5/group) were given a single IC infusion of the indicated viruses in log increments per group ranging from 10²-10⁷ pfu. For the intravenous (IV) roa, groups of five 6-8 week old female BALB/c mice were given a single IV injection of the indicated viruses into the tail vein, in half log increments per group ranging from 3×10⁶-3×10⁹ pfu, diluted into 100 μL per injection. Following IC or IV injections, mice were monitored daily for signs of distress including weight loss, piloerection, hind-limb paralysis and respiratory distress. The median lethal dose (LD50) was calculated using the Spearman Karber method, while the maximal tolerable dose (MTD) was denoted as the highest dose not resulting in a single animal death.

Imaging glioblastoma in an animal model: U87MG and CT2A cells were adapted for bioluminescent imaging by transducing with lentivirus containing firefly luciferase (FLUC) and transfecting FLUC plasmid respectively. U87MG FLUC and CT2A FLUC cells were injected IC into CD1 nude and C57BL/6 respectively. Animals with FLUC expressing tumours were monitored for tumour progression using the live imaging IVIS Xenogen 200 system after an IP injection of luciferin (Gold Biotechnology Inc). The animals were monitored for signs of distress including survival, weight loss, morbidity, piloerection, hind-limb paralysis and respiratory distress.

Mouse syngeneic glioblastoma tumour models: Brain tumours were established by a single stereotactic injection with CT-2A mouse glioma cells into 6-8 week old C57BL/6 animals. Five days post injection. On Day 19 C57BL/6 mice bearing CT-2A tumours were IV treated with 6 doses of FMT (5×10⁸ pfu/dose thrice weekly) or injected stereotactically with FMT (2×10⁷ in a volume of 50 μl) using an infusion pump (rate=3 μl/min). Some C57Bl/6 animals were sacrificed at day 19 and images were captured on a Nikon dissecting microscope. The remaining animals were monitored for survival.

Human glioblastoma xenograft model: Human ovarian U87MG cells were adapted for bioluminescent imaging at which time 1e6 U87MG cells were injected IC into 6-8 week old athymic CD-1 nude mice. Untreated CD-1 animals develop tumours at about day 15-21. Mice were either treated with a single intravenous (tail vein) injection performed on day 14 with FMT (5×10⁶), or treated IC with the same viruse at a dose of 2×10⁷ pfu. Animals were monitored for survival and for signs of distress including weight loss, morbidity, piloerection, hind-limb paralysis and respiratory distress. Tumour imaging was captured with a Xenogen 200 IVIS system (Caliper LS, USA).

Rotorod: Balb/C mice were tested for motor function/performance on a rotating rod apparatus prior to IC viral administration. Mice were placed on a rotorod for 3 trials per day for 4 consecutive days. After allowing the animals 0.5 min to adjust to the apparatus, the rod was accelerated in a linear fashion 0.1 rpm/s. Latency to fall was measured in minutes. The animals were divided into groups of 3. Motor function one week post surgery in uninjected (Naïve). PBS and FMT IC treated animals. Standard error of the mean was calculated.

Nucleic Acid Sequencing: FMT sequencing was performed at the Ontario Institute for Cancer research (Toronto, Canada) on FMT cDNA which was generated using a shotgun approach with random hexamers on trizol extracted and RNeasy purified FMT RNA.

Protein sequencing: FMT virus was amplified in Vero cells to high titer (˜10¹¹ pfu/mL), purified, and lysed with 5× Laemmli sample buffer (60 mM Tris-Cl pH 6.8, 2% SDS, 10% glycerol, 5% β-mercaptoethanol, 0.01% bromophenol blue) and separated on 12% SDS-PAGE gels. Replicate gels were stained with either coomasie blue or silver, and nine bands were extracted for peptide sequencing.

Manufacturing and rescuing recombinant FMT virus: Recombinant FMT was produced as described recently for Maraba virus25. Briefly. FMT virus complementary DNA (cDNA) was amplified in three separate RT-PCR reactions yielding overlapping fragments that were stitched together using internal restriction sites. The full length ˜11 Kb cDNA was then cloned into a modified LC-KAN vector (Lucigen, Middleton, Wis.) carrying a T7 promoter upstream of the 5′-antigenomic leader sequence and immediately downstream of the 3′-terminator a modified hepatitis delta virus ribozyme and T7 polymerase termination signal sequence. A549 lung carcinoma cells seeded at 3.0×10⁵ cells/well in 6-well plates were infected 24 hr later with vaccinia virus (moi=10) expressing the T7 RNA polymerase37 in OptiMeM medium for 1.5 hours. Following removal of the vaccinia virus, each well was transfected with LC-KAN FMT (2 μg) together with pCI-Neo constructs encoding for FMT “N” (1 μg), “P” (1.25 μg), and L (0.25 μg) with lipofectamine 2000 (5 μl per well) according to the manufacturer's instructions. The transfection reagent was removed 5 hr later and replaced with DMEM containing 10% HI-FBS. At 48 hours following the transfection, medium was collected (pooled from two plates), filtered (0.2 μm) to remove contaminating vaccinia virus, and 1 ml was used to infect SNB19 glioblastoma cells in each well of a 6-well plate. Cytopathic effects and GFP expression visible 24-48 hours later were indicative of a successful rescue. Recombinant FMT underwent three rounds of plaque purification (on SNB19 cells), before scale up, purification on sucrose cushion, and resuspension in PBS containing 15% glucose.

Phylogenetic Analysis: Phylogenetic relationships between rhabdoviruses based on a Muscle alignment of L protein amino acid sequences, and using the paramyxovirus Measles Edmonston strain as the outgroup. The tree was generated by the neighbor-joining method and bootstrap values (indicated for each branch node) were estimated using 1000 tree replicas. Branch lengths are proportional to genetic distances. The scale bar corresponds to substitutions per amino acid site.

Immunoblotting: Cells were lysed (50 mM Tris-HCl; 150 mM NaCl; 1% Triton) X-100; 1% SDS) and protein quantified using the Lowry assay (Bio-Rad). Total cell lysates were prepared in SDS sample buffer, and 5-50 μg of total protein was separated by SDS-PAGE on Bis-Tris gels (ranging from 8-15%) and transferred to nitrocellulose or PVDF membranes. Membranes were probed with primary antibodies diluted in 5% skim milk powder (SMP) or 5% Bovine Serum Albumen (BSA) overnight at 4 deg C., followed by horse radish peroxidase-conjugated secondary antibodies diluted in 5% SMP for 1 hr at room temperature. The following primary antibodies were used: rabbit anti-PARP (Cell Signaling, 9542); mouse anti-caspase 3 (Cell Signaling, 9668); mouse anti-caspase 8 (Enzo Life Sciences, 12F5); rabbit anti-caspase 9 (Cell Signaling, 9502); rabbit anti-BID (Cell Signaling, 2002); mouse anti-GAPDH (R&D Systems). A polylonal anti-FMT antibody was generated in rabbits (Capralogics Inc.) using purified, UV-inactivated FMT virus. Protein bands were visualized using SuperSignal West Pico Chemiluminescent Substrate System (Pierce Biotechnology)

CD8+ T cell depletion: The brains of 7 week old C57BL/6 mice were stereotactically implanted with 2e5 CT2A cells that express firefly luciferase (CT2Afluc). Mice were treated with 2e7 PFU of Farmington virus at the site of tumour implantation 7 days later. For CD8+ T cell depletion studies, 200 μg of anti-mouse CD8 antibody (clone 2.43) was injected intraperitoneally (IP) one day prior to virus treatment and 100 μg on the day of treatment. A maintenance dose of 100 μg every 3 days was given for the following 2 weeks.

Statistics: For Kaplan Meier plots, survival plots were compared using Mantel-Cox Log rank analysis (Graphpad Prism).

EXAMPLES Example 1 Farmington Virus is not a Vesiculovirus

The full-length genomic sequence for FMT was determined. The sequence of the complementary DNA (cDNA) polynucleotide produced by FMT is shown in SEQ ID NO: 1. The RNA polynucleotide of FMT is shown in SEQ ID NO: 2. Five putative open reading frames were identified in the genomic sequence. Additional ORFs may be present in the virus that have not yet been identified. The sequences of the corresponding proteins are shown in SEQ ID NOs: 3, 4, 5, 6 and 7, and the encoding DNA sequences are shown in SEQ ID NOs: 8, 9, 10, 11 and 12, respectively. Phylogenetic analysis of the full-length genomic sequence was performed by aligning the amino acid sequence of the putative FMT L protein to the L protein sequences of representative members from the 6 genera of Rhabdoviridae (FIG. 1). The alignment demonstrated that FMT did not appear to belong to the current 6 genera schema of the Rhabdoviridae family. FMT virus appears to be more divergent from the currently known rhabdoviruses. While we did detect some sequence homology (˜50% identity) between a short segment of the L protein of FMT and lettuce necrosis yellow virus, we were unable to detect any homology of the 4 remaining FMT putative open reading frames (ORFs) (N, P. G. M) to any sequences in the NCBI database. This suggests that FMT, which was originally classified incorrectly as a vesiculovirus (Tesh et al. Emerging Infect. Dis. 2002), may in fact constitute the type member of a new genus within the Rhabdoviridae family (FIG. 1; and see Table 2 and accompanying Sequence Listing file).

TABLE 2 Description of Sequences. SEQ ID NO. 1 Farmington rhabdovirus - DNA cDNA produced by the FMT rhabdovirus SEQ ID NO. 2 Farmington rhabdovirus - RNA SEQ ID NO. 3 Farmington rhabdovirus ORF 1 The promoter is at position 134 to 149 and the encoding sequence is at positions 206 to 1444 of SEQ ID NO: 1 SEQ ID NO. 4 Farmington rhabdovirus ORF 2 The promoter is at position 1562 to 1578 and the encoding sequence is at positions 1640 to 2590 of SEQ ID NO: 1 SEQ ID NO. 5 Farmington rhabdovirus ORF 3 The promoter is at positions 2799 to 2813 and the encoding sequence is at positions 2894 to 3340 of SEQ ID NO: 1 SEQ ID NO. 6 Farmington rhabdovirus ORF 4 The promoter is at positions 3457 to 3469 and the encoding sequence is at positions 3603 to 5717 of SEQ ID NO: 1 SEQ ID NO. 7 Farmington rhabdovirus ORF 5 The promoter is at positions 5766 to 5780 and the encoding sequence is at positions 5832 to 12221 of SEQ ID NO: 1

SEQ ID NO: 3 is encoded by SEQ ID NO: 8 (i.e. the encoding sequence of positions 206 to 1444 of SEQ ID NO: 1). SEQ ID NO: 4 is encoded by SEQ ID NO: 9 (i.e. the encoding sequence of positions 1640 to 2590 of SEQ ID NO: 1). SEQ ID NO: 5 is encoded by SEQ ID NO: 10 (i.e. the encoding sequence of positions 2894 to 3340 of SEQ ID NO: 1). SEQ ID NO: 6 is encoded by SEQ ID NO: 11 (i.e. the encoding sequence of positions 3603 to 5717 of SEQ ID NO: 1). SEQ ID NO: 7 is encoded by SEQ ID NO: 12 (i.e. the encoding sequence of positions 5832 to 12221 of SEQ ID NO: 1).

FIG. 1 shows A) Schematic of where FMT was first isolated in 1969. B) Amino acid Blast alignment of 5 FMT ORFs reveals no sequence homology to any other sequences in the database except for the L protein which is ˜45% similar to plant rhabdovirus: Lettuce Necrotic yellow virus (LNYV). C) Commassie stained SDS PAGE gel of FMT virus showing 4 of the 5 predicted FMT ORF proteins. These bands were excised from the gel and their identity confirmed through protein sequencing by tandem mass spectrometry. D) Phylogenic tree derived from the amino acid sequences of the polymerase genes of various rhabdoviruses. The Measles paramyxovirus was included as a non-family control. All previous oncolytic rhabdoviruses have been identified from the vesiculovirus genus (VSV, Maraba). Unexpectedly, Farmington virus appears to cluster with the plant infecting cytorhabdoviruses. E) We have built a recombinant system for the FMT platform that allows us complete control of the genetic make-up of the virus. We show here the generation of a fully replicative GFP expressing FMT strain as an example. F) Electron microgram of FMT bullet shaped virion measuring 55 nm×150 nm. (adapted from Tesh et al. Emerging Infect. Dis. 2002).

Example 2 Farmington Virus does not Demonstrate Neurotoxicity

FMT demonstrated profound attenuation in non-transformed cells in vitro. To ascertain whether the observed attenuation in vitro translates to safety in vivo, we injected stereotaxically into the right striatum of the brain increasing doses of rhabdoviruses and monitored for signs of neurotoxicity (including weight loss, piloerection, hind leg paralysis, morbidity and mortality). FMT had an LD₅₀ of approximately 1×10⁹ in contrast the other rhabdoviruses displayed LD₅₀ of approximately 10², (FIG. 2A). The Maximum Tolerated Dose (MTD) was determined to be the highest dose not resulting in durable morbidity. (FIG. 2A). For FMT the MTD was approximately 1×10^(7.5) pfu while for the other rhabdoviruses the LD₅₀ occurred at such a low dose of virus the MTD was impossible to determine. These animals displayed clinical signs of a CNS infection with rapid and progressive weight loss, hind leg paralysis and had significant titres of virus in their brain just prior to death (data not shown).

Although we found no acute neurotoxicity from IC treatment with FMT, we wished to assess the cognitive and motor function of the mice several days after virus infection. Therefore, we assessed the motor function before and after treatment with these wild-type FMT virus using a rotorod apparatus (FIG. 2B). Specifically, we measured the latency of these animals to fall from a slowly accelerating rod. We show that there is no significant difference in the latency to fall between the mock-infected animals or virus infected animals, 1 week prior and 1 week post injection (FIG. 2B).

In addition to intracranial toxicity, we evaluated the toxicity of FMT when administered intravenously (IV) in immunocompetent mice with escalating doses of virus (FIG. 2C). FMT is well tolerated IV and never reaches an LD₅₀ even at our highest dose 3×10⁹ pfu which is comparable to an attenuated version of Maraba we described in Brun, J. et al. Identification of Genetically Modified Maraba Virus as an Oncolytic Rhabdovirus. Mol Ther 18, 1440 (2010). FMT animals IV dosed at greater than 3×10⁸ pfu displayed transient weight loss and moderate piloerection, which resolved 5-7 days post treatment (data not shown). No detectable titres were observed from brain homogenates taken from FMT treated animals 3 months post IV treatment (FIG. 2D). In addition, following administration of high doses of FMT (1×10⁷ pfu) in the brain, we found no signs of cell death and comparable inflammatory responses to those of saline injected control mice (FIG. 2E). This differed dramatically from VSV injected animals, which displayed a striking increase in inflammatory cells, condensed nuclei, and a perforated morphology. Due to its lack of neurotoxicity and potent CNS tumour killing capacity, we elected to proceed with FMT as a platform to develop as a novel oncolytic against GBM.

FIG. 2 shows the FMT Safety Profile A) Groups of 5 Balb/C mice were injected sterotaxically into the right striatum of the brain with increasing doses of rhabdoviruses as indicated and monitored for signs of distress including weight loss, piloerection, hind leg paralysis, morbidity and mortality. Maximal Tolerable Dose (MTD) was determined to be the highest dose not resulting in durable morbidity as measured by behaviour and weight. LD₅₀ was determined using the Spearman Karber method. FMT is unique among rhabdoviruses as a non-neurotoxic virus. B) To detect any cognitive deficiencies in the striatum, motor function was assessed by rotorod apparatus which measures latency to fall off an accelerating rod. Motor function is indistinguishable from controls after intracerebral injection of FMT. C) Groups of 3-5 Balb/C mice were injected once intravenously in half log increments of virus ranging from 3×10⁶ pfu to 3×10⁹ pfu. The animals were monitored for signs of distress including weight loss, morbidity, piloerection, hind-limb paralysis and respiratory distress. FMT shows a very high MTD of 1×10⁹ pfu when delivered systemically. D) Animals sacrificed 3 months post-intracerebral inoculation demonstrate no viable virus in the brain homogenates. Limit of detection is 101. E) Balb/C mice were inoculated intracerebrally with the indicated viruses (1×10⁷ pfu) and sacrificed 2 days post treatment. Little to no inflammation is visible and no cell loss is detectable following FMT treatment. This is in contrast to VSV which shows significant neuronal loss (empty spaces, inset).

Example 3 Farmington Virus Potently and Selectivity Kills Brain Tumour Cells

Wild-type FMT isolates demonstrate attenuation in normal primary cells while maintaining potent glioma cell killing capacity (FIG. 3A). To evaluate the clinical relevance of our novel oncolytic rhabdoviruses to treat brain cancer, we examined whether FMT could kill freshly derived patient tumour samples. Cell cultures isolated from 3 patients with primary glioblastoma multiforme were infected with FMT and 48 h later, viability assays demonstrated that FMT virus was potently cytotoxic to 2 of 3 patient tumour explants (FIG. 3A). To test the killing capacity of the FMT isolates we performed cell killing assays on normal human astrocytes (NHA) and 3 GBM tumour cell lines (FIG. 3B). While wild type MRB was very potent against all of the GBM cell lines, it was also highly lytic against both primary normal human astrocytes (NHA). Remarkably, FMT demonstrated the greatest therapeutic index, with potency rivaling MRB in the majority of GBM lines while remaining highly attenuated in NHA and GM38 primary cell lines (FIG. 3C). This demonstrates that FMT virus is a potent and selective oncolytic virus when tested against brain cancer cell lines.

In FIG. 3 we show A) Summary of FMT in vitro cytotoxicity showing potent activity against primary glioblastoma patient samples and established human and mouse brain tumour cell lines, while remaining attenuated against normal cells. B) FMT is a potent and selective killer of glioblastoma cell lines. Viability was assayed using Alamar blue assay 72h post treatment. Error bars represent SEM of 4 biological replicates. C) Detailed assessment of FMT potency against tumour and normal cells. EC50 (moi=multiplicity of infection) represents the ratio of virus:cell required to kill 50% of cultured cells in a 72 time frame as measured using an Alamar Blue viability assay.

Example 4 Farmington Virus is Efficacious in Xenograft and Syngeneic Models of Glioblastoma

We next sought to determine the in vivo efficacy of our candidate viruses in mouse models of glioblastoma. After adapting human U87MG glioma cells for bioluminescent imaging, we established an intracerebral U87MG glioma model in athymic mice and we examined the IV and IC efficacy of FMT in this model (FIG. 4A-B). Specifically, animals were treated with a single FMT dose IC (1×10⁵) or IV (5×10⁸ pfu) 14 days post implantation. Three days after the first treatment we observed a significant decrease in tumour burden with a greater decrease observed by day 7 (FIG. 4A). Interestingly the spinal metastases in this model are completely cleared in all tumour bearing animals. In contrast, animals treated with UV inactivated virus had a significant increase in tumour burden by day 7 at which point they started exhibiting neurological symptoms from their brain tumours (FIG. 4B). All IV treated animals responded to treatment with 4 of 11 durably cured and surviving beyond 100 days post treatment. Most IC treated animals responded to treatment (10 of 16) with a significant (˜2 fold) increase in time to death. Moreover we also used fluorescent microscopy to visualize tumour explants of mock-infected animals and durably cured animals. While we detect a strong GFP expressing glioma tumour in mock-infected animals, there is a clear absence of GFP signal in FMT treated animals (FIG. 4C). To complement our studies of viral efficacy in immunocompromised animals, we tested FMT in a mouse CT-2A syngeneic glioma model. Unlike xenograft models in which human gliomas grow expansively. CT-2A gliomas are infiltrative similar to what is observed clinically. We established the CT-2A glioma model by stereotactically injecting 2×10⁵ cells into the striatum (right frontal lobe) of C57BL/6 mice. Since treatments typically commence in human patients after they present with clinical symptoms of GBM, we sought to examine the effect of FMT at exactly the time when animals exhibit outward symptoms. In the CT-2A animals begin to show symptoms 15-20 days post implantation. These symptoms include increased intracranial pressure, lethargy, motor function, piloerection, and hunched posture. Accordingly, 19 days post implantation C57BL/6 animals were treated with FMT IV (5×10⁸ pfu thrice weekly for 2 weeks) or with a single IC dose of FMT (2×10⁷ pfu). Most animals responded to both the treatment regimens, durable cures achieved in 3 of 11 IC and 2 of 10 IV treated animals in this challenging model of advanced GBM (FIG. 4D). Thus FMT virus demonstrates efficacy in preclinical models of brain cancer.

FIG. 4 shows FMT In Vivo Efficacy in Preclinical Models of Glioblastoma A) Bioluminescence-adapted U87MG human gliomblatsoma cells (1e6) were stereotxically implanted into right striatum of CD-1 nude mice. After 2 weeks animals were either treated with a single dose of FMT intravenously (IV—5×10⁸ pfu) or intracranially (IC—1×10⁵ pfu) and monitored by IVIS bioluminescence imaging. Disseminated tumours in all mice treated with FMT regress rapidly within 3-7 days and become undetectable in the spinal cord. B) Kaplan Meir survival plot of animals treated with a single dose IC (1×10⁵ pfu) resulting in a doubling of mean time to death (Log rank test p=0.0001) or IV (5×10⁸ pfu) resulting in durable cures in 40% of animals (Log rank test p=0.0001). C) Fluorescence micrograph of a mock infected mouse brain with an orthotopic GFP tagged U87MG tumour (top 2 panels) versus a FMT treated brain (bottom 2 panels). GFP expressing tumour is clearly visible in sagittal sections of untreated mice, while FMT treatment results in no detectable GFP tumour signal, confirming tumour regression. D) Syngeneic mouse glioblastoma tumour model using the CT2A cell line. Here again, tumours were allowed to establish until the point where mice began to die from their tumour burden. Both IC (one dose 2×10⁷ pfu) and IV (6 doses 5×10⁸) treatment doubled mean time to death and resulted in >20% durable cures.

Example 5 Farmington Virus Induces Anti-Tumour Immunity

Emerging evidence is demonstrating that the oncolytic effect of many viruses, including oncolytic rhabdoviruses, is due in part to the induction of anti-tumor immunity. To explore the possibility that FMT virus induces multiple mechanisms for tumor destruction in vivo, we asked whether treating immunocompetent tumor-bearing mice with FMT virus evokes anti-tumor immunity. To begin, we performed a “re-challenge” experiment, where C57/BL6 mice previously harboring CT-2A tumors that had been successfully treated with IC FMT virus infusions were injected for a second time with CT-2A cells directly into the brain. In these experiments, previously cured mice uniformly rejected the cells (FIG. 5A), demonstrating that they had acquired long-lasting immunity towards CT-2A antigen(s). Next, we examined the role of cytotoxic T-lymphocytes (CTLs) in the anti-tumor response elicited by FMT virus. Mice were inoculated with CT-2A cells in their brain, and then CTLs were removed using antibodies directed towards CD8 concomitant with FMT virus treatment. Consistent with recent data from other labs using different oncolytic agents, these experiments showed that FMT virus induced complete responses only when CTLs were present (FIG. 5B). Thus, in addition to directly lysing MG cells, these data demonstrate that FMT virus induces a potent and long-lasting CTL-mediated anti-MG immune response in immunocompetent mice.

In FIG. 5A, C57/B6 mice were implanted with CT2A murine glioma cells into the striatum (3×10⁵ cells). Mice were treated with a single dose of FMT (2×10⁷ pfu) and subsequently cured of their initial tumour. After 6 months, these mice were challenged with CT2A cells implanted into the striatum. Naive mice were implanted with CT2A cells as a control. Bioluminescent imaging to monitor CT2A tumour growth showed that mice that had previously been cured of the tumours completely rejected subsequent CT2A tumour growth, while naive mice grew tumours with the expected kinetics. In FIG. 5B) C57/B6 mice were implanted with CT2A murine glioma cells into the striatum (3×10⁵ cells) and allowed to grow tumours for 14 days. One group mice received anti-CD8 polyclonal serum injections to remove CD8+ T cells or matched pre-immune serum as a control. Both groups were treated with a single intracranial dose of FMT (2×10⁷ pfu) to induce tumour regressions. All mice responded with tumour regression as measured using bioluminescent tumour imaging (not shown), but mice that had been stripped of their CD8+ T cells all eventually regrew tumours and failed therapy.

Example 6 Farmington Virus Productively Infects Tumor and Normal Cells

Without exception, the therapeutic index associated with existing oncolytic viruses is due to differential infection and/or productivity in tumor versus normal cells. In the case of rhabdoviruses, current oncolytic strains can “sense” cancer-specific defects in type I IFN signalling, which renders them selectively productive in transformed cells. Unfortunately, current oncolytic rhabdoviruses are highly neurotoxic when delivered local-regionally into the CNS. Given that FMT virus is safe when infused IC and is genetically very distinct from the existing agents, we suspected that its mechanism for tumor-specific destruction must be something other than heightened productivity secondary to IFN defects in tumor cells. To begin to evaluate this hypothesis, we infected SNB19 and NHA cells with rec-FMT-GFP virus and evaluated GFP expression and viral protein production over time. Fluorescence microscopy and immunoblot analyses clearly demonstrated that FMT virus does not distinguish tumor from normal via differential infectivity or viral protein production (FIG. 6A-B). Specifically, both GFP and FMT protein expression became easily detectable 6.5-16 hours after infection and continued to be strongly expressed 72 hours later, irrespective of the transformed state of the infected cell line. In parallel, we performed one-step growth evaluation of FMT virus in various tumor and normal cell lines to examine productivity. These experiments showed that infectious FMT virus particles are produced quickly (within 6:5 hours) and to high titers (˜10⁸ pfu) in both tumor and normal cell lines (FIG. 6B). Collectively, these date demonstrate that, in stark contrast to the existing VSV Δ51 and Maraba MG1 series of oncolytic rhabdoviruses. FMT virus is equally productive in normal as compared to tumor cells.

We thus interrogated the interaction between FMT virus and the type I interferon response. GFP-expressing rec-FMT or Maraba-Δ51 virus was added at low moi to a GM38 cell monolayer, and plaque and infectious foci size were measured. As expected, Maraba-Δ51 infection did not infect or kill GM38 cells unless the innate immune response was blocked a priori by treatment with the type I interferon inhibitor B18R protein derived from vaccinnia virus (VV-B18R; FIG. 6C-D). In contrast, FMT virus formed moderately-sized infectious foci in the GM38 cells, but did not kill them, and was unaffected by B18R pre-treatment. Furthermore, unlike Maraba-Δ51. FMT virus completely blocked type I interferon production in PC3 cells as measured in an interferon bioassay (FIG. 6E). Collectively, these results indicate that, in contrast to the current arsenal of genetically engineered oncolytic rhabdoviruses. FMT virus potently blocks the human type I interferon response and can productively infect both normal and tumor cell lines, which points towards a novel cancer-selective mechanism for this oncolytic agent.

In FIG. 6 is shown A) Western blot demonstrating similar kinetics of FMT virus infection and protein production in both human brain tumour cells (SNB19) and primary normal human astrocytes (NHA). B) Single step growth curve showing identical virus replication and virion productivity from tumour (SNB19) and normal (NHA) cells following infection with FMT. C) Fluorescence Microscopy of GFP-expressing rec-FMT or Maraba-Δ51 virus added to a GM38 cell monolayer, and plaque and infectious foci size were measured showing that Maraba-Δ51 infection did not infect or kill GM38 cells unless the innate immune response was blocked by treatment with the type I interferon inhibitor B18R protein derived from vaccinnia virus (VV-B18R) while FMT virus formed infectious foci in GM38 cells and was unaffected by B18R pre-treatment. D) Size of Infectious foci determined from fluorescence microscopy. E) Interferon bioassay in PC3 cells shows that unlike Maraba-Δ151. FMT blocks type I interferon production.

Example 7 Farmington Virus Selectively Induces Apoptosis in Tumor Cells

We used the NT2 cell system that consists of transformed NT2 teratocarcinoma cells which can be induced to differentiate into post mitotic neurons with retanoic acid. Following infection with wild type VSV or FMT we observed that these viruses infected and produced infectious progeny to the same degree in either cancerous or non-cancerous forms of the NT2 cells (FIG. 7A). However, although these viruses were potently cytotoxic to malignant NT2 cells, FMT showed almost no cytotoxicity in differentiated post mitotic NT2 cells (FIG. 7B). This indicated that in contrast to other oncolytic rhabdoviruses like VSV. FMT virus appeared to have a unique mechanism of tumour selectivity functioning at the level of cytotoxicity.

Rhabdoviruses kill permissive cells by apoptosis, activated through virus-mediated degradation of key BH3-only proteins, an event which ultimately engages the apical intracellular and extracellular caspases that initiate the irreversible cell death cascade. To ascertain whether FMT virus selectively kills tumor cells via differential induction of apoptosis, we evaluated the activation status of key proteins in the apoptotic heirarchy. As expected, the surrogate apoptosis marker PARP as well as the downstream effector caspase 3 were strongly activated in SNB19 but not NHA cells treated with FMT virus (FIG. 7C), indicating the presence of apoptosis. Moreover, the activator caspases 8 and 9 were engaged in the tumor cells, but not in the normal cells. The NT2 cell system data is consistent with this apoptosis data in the transformed versus normal cell lines showing that cell death induced by FMT virus is dependent not on the productivity of the virus infection within, but rather the anti-apoptotic threshold of, the infected cell.

In FIG. 7A, both pre and post differentiated cell types were permissive to infection by wt VSV and wt FMT virus, producing infectious particles in the 10⁶-10⁸ range. B) shows that only VSV was cytolytic against the neuron. C) Western blot of several components of the cellular apoptotic signaling cascade following infection of either tumour (SNB19) or normal cells (NHA). FMT appears to initiate the activation (cleavage) of Caspase 8, Caspase 9, BID, and PARP only in tumour cells. To our knowledge, this is the first report of an oncolytic virus whose activity is restricted not at the level of infectivity, but at the level of selective initiation of cell death. D) Schematic of cellular apoptosis signaling cascade. Proteins that are cleaved during activation are depicted in orange and correspond to those included in our western blotting array in panel C.

In the preceding description, for purposes of explanation, numerous details are set forth in order to provide a thorough understanding of the examples. However, it will be apparent to one skilled in the art that these specific details are not required. Equivalent changes, modifications and variations of some examples, materials, compositions and methods can be made within the scope of the present technology, with substantially similar results.

The above-described examples are intended to be exemplary only. Alterations, modifications and variations can be effected to the particular embodiments by those of skill in the art without departing from the scope, which is defined solely by the claims appended hereto. 

1. A pharmaceutical composition comprising an isolated viral particle having a genome comprising open reading frames that encode: a protein comprising SEQ ID NO: 3; a protein comprising SEQ ID NO: 4; a protein comprising SEQ ID NO: 5; a protein comprising SEQ ID NO: 6; and a protein comprising SEQ ID NO:
 7. 2. (canceled)
 3. The pharmaceutical composition according to claim 1, wherein the open reading frames encode: a protein consisting of SEQ ID NO: 3; a protein consisting of SEQ ID NO: 4; a protein consisting of SEQ ID NO: 5; a protein consisting of SEQ ID NO: 6; and a protein consisting of SEQ ID NO:
 7. 4. (canceled)
 5. (canceled)
 6. The pharmaceutical composition according to claim 1, wherein the isolate viral particle further comprises at least one additional open reading frame for encoding at least one additional protein.
 7. The pharmaceutical composition according to claim 6 wherein the additional protein is an immunogenic protein.
 8. A pharmaceutical composition comprising an isolated viral particle capable of producing a cDNA polynucleotide when the virus is in a host cell, the cDNA polynucleotide comprising: SEQ ID NO: 8, or a variant thereof comprising one or more silent substitutions; SEQ ID NO: 9, or a variant thereof comprising one or more silent substitutions; SEQ ID NO: 10, or a variant thereof comprising one or more silent substitutions; SEQ ID NO: 11, or a variant thereof comprising one or more silent substitutions; SEQ ID NO: 12, or a variant thereof comprising one or more silent substitutions.
 9. (canceled)
 10. (canceled)
 11. A pharmaceutical composition comprising an isolated viral particle capable of producing a cDNA polynucleotide comprising SEQ ID NO: 1 when the virus is in a host cell.
 12. A pharmaceutical composition comprising an isolated viral particle comprising an RNA polynucleotide comprising SEQ ID NO:
 2. 13. The pharmaceutical composition according to claim 1, wherein the pharmaceutical composition comprises a sufficient number of isolated viral particles to provide at least 1e5 plaque forming units (pfu) of the viral particles.
 14. The pharmaceutical composition according to claim 8, wherein the cDNA polynucleotide further comprises at least one promoter sequence. 